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- PDB-6s3p: Crystal structure of helicase Pif1 from Thermus oshimai in comple... -

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Basic information

Entry
Database: PDB / ID: 6s3p
TitleCrystal structure of helicase Pif1 from Thermus oshimai in complex with (dT)18
Components
  • DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • PIF1 helicase
KeywordsHYDROLASE / DNA helicase
Function / homology
Function and homology information


telomere maintenance / DNA helicase activity / DNA repair / nucleotide binding / metal ion binding
Similarity search - Function
: / DNA helicase Pif1-like / PIF1-like helicase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / DNA (> 10) / PIF1 helicase
Similarity search - Component
Biological speciesThermus oshimai (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.926 Å
AuthorsDai, Y.X. / Chen, W.F. / Teng, F.Y. / Liu, N.N. / Hou, X.M. / Dou, S.X. / Rety, S. / Xi, X.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370798,11304252,11574252,31301632 China
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural and functional studies of SF1B Pif1 from Thermus oshimai reveal dimerization-induced helicase inhibition.
Authors: Dai, Y.X. / Chen, W.F. / Liu, N.N. / Teng, F.Y. / Guo, H.L. / Hou, X.M. / Dou, S.X. / Rety, S. / Xi, X.G.
History
DepositionJun 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 28, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PIF1 helicase
B: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)55,7702
Polymers55,7702
Non-polymers00
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-15 kcal/mol
Surface area20310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.850, 64.583, 144.296
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PIF1 helicase


Mass: 50339.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus oshimai (bacteria) / Gene: Theos_1468 / Plasmid: pET15b-SUMO / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): C2566H / References: UniProt: K7RJ88
#2: DNA chain DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 5430.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus oshimai (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Tris-HCl 0.1M NaF 0.03M NaI 0.03M NaBr 0.03M MES 0.03M PEG 4K 10% Glycerol 20%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.926→37.73 Å / Num. obs: 38861 / % possible obs: 88.12 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 32.55 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0557 / Rpim(I) all: 0.02295 / Rrim(I) all: 0.0603 / Net I/σ(I): 21.62
Reflection shellResolution: 1.926→1.995 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.4628 / Mean I/σ(I) obs: 4.01 / Num. unique obs: 2388 / CC1/2: 0.937 / Rpim(I) all: 0.2079 / Rrim(I) all: 0.5095 / % possible all: 55.48

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Processing

Software
NameVersionClassification
PHENIX(1.14rc1_3177: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FTD

5ftd


Resolution: 1.926→37.73 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 22.75
RfactorNum. reflection% reflectionSelection details
Rfree0.2072 1893 4.9 %5%
Rwork0.1741 ---
obs0.1757 38651 88.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.926→37.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3504 141 0 413 4058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093741
X-RAY DIFFRACTIONf_angle_d0.9265105
X-RAY DIFFRACTIONf_dihedral_angle_d23.3181431
X-RAY DIFFRACTIONf_chiral_restr0.059563
X-RAY DIFFRACTIONf_plane_restr0.007643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.926-1.97420.3142570.24721259X-RAY DIFFRACTION42
1.9742-2.02760.27431460.20792696X-RAY DIFFRACTION92
2.0276-2.08720.273870.20761770X-RAY DIFFRACTION61
2.0872-2.15460.22531590.19462929X-RAY DIFFRACTION100
2.1546-2.23160.20891510.22936X-RAY DIFFRACTION100
2.2316-2.3210.25531160.21322091X-RAY DIFFRACTION71
2.321-2.42660.22451270.19522963X-RAY DIFFRACTION100
2.4266-2.55450.24161390.1932975X-RAY DIFFRACTION100
2.5545-2.71450.20781480.18922526X-RAY DIFFRACTION86
2.7145-2.92410.22311690.19392962X-RAY DIFFRACTION100
2.9241-3.21830.24741410.18363008X-RAY DIFFRACTION100
3.2183-3.68380.17621580.16462614X-RAY DIFFRACTION88
3.6838-4.64060.1691610.1392988X-RAY DIFFRACTION98
4.6406-46.52860.20711340.16473041X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.1375-3.05091.44684.7797-0.19764.4703-0.1473-0.0820.12060.4450.0951-0.31910.29190.09620.03030.4155-0.05410.07530.3094-0.02750.2139-9.98374.2517-3.4473
21.7617-0.32070.34462.4625-0.67982.73890.0583-0.0132-0.19730.1413-0.01580.3330.2898-0.162-0.02420.2014-0.04080.03740.1986-0.04470.2272-15.21233.1122-23.1745
32.99611.39650.51371.30260.08261.10620.1698-0.2690.09850.5251-0.19750.0193-0.0655-0.04230.03490.42160.00630.00020.2696-0.0620.265-3.43519.9421-9.7456
41.3886-0.53140.18862.23770.39781.88770.0410.11440.0122-0.0121-0.0009-0.1216-0.05020.1102-0.06020.1607-0.00740.00240.2151-0.01970.20458.9416.2109-33.4639
54.03830.3529-0.00472.5130.23421.6082-0.1068-0.08420.08260.34720.09610.0019-0.0168-0.00450.0160.3108-0.0094-0.04010.1748-0.04260.16190.934721.2673-16.6397
65.9587-0.96070.1770.1672-0.30066.6742-0.19560.47270.558-0.41640.12660.4637-0.3164-0.20860.03640.21870.0315-0.04580.2732-0.00860.2508-0.824712.5509-31.8863
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 68 through 108 )
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 231 )
3X-RAY DIFFRACTION3chain 'A' and (resid 232 through 286 )
4X-RAY DIFFRACTION4chain 'A' and (resid 287 through 435 )
5X-RAY DIFFRACTION5chain 'A' and (resid 436 through 502 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 8 )

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